It seemed the perfect solution to the problem of Leonardo, Raphael, Michelangelo and Donatello. Thousands of red-eared terrapins had been dumped in Britain's waterways in the early 1990s, after being bought as pets during the Teenage Mutant Ninja Turtle craze.

Rather than allow them to devour native animals including fish, newts, moorhens and ducklings, a terrapin charity paid for more than 800 to be flown abroad to start a new life in Italy.

The terrapins took up residence at an idyllic site, a sanctuary in Massa Marittima, 90 miles south of Pisa. However, after the eviction last year of the sanctuary's manager hundreds of the rescued reptiles are dead or dying, while scores more of the non-native animals have escaped into the Tuscan countryside, according to local people and terrapin experts.

The Italian sanctuary, known as Carapax, or the European Centre for Chelonian Conservation, and run by Donato Ballasina, the director, attracted funds from charities across Europe. It received £25 for every terrapin and other non-native chelonian sent to the centre.

"This was a shipping of animals to their death – to be put in lakes which were not fit for purpose," said Tom Langton, an independent ecologist who investigated the project. "Animals were underfed and dying with disease. The whole thing is bizarre and worrying."

In Britain, there are more than 2,000 terrapins still at large in waterways in the London area alone. Many are dinner plate-sized red-eared terrapins (Trachemys scripta elegans), also called sliders, which were discarded by their Ninja Turtle-loving owners. Red-eared terrapins are now banned from sale in Britain but many enthusiasts have switched to other similar non-native species.

In 2007, the City of London Authority captured rogue terrapins from park ponds in the capital and, along with other organisations and individuals, passed them to the British Chelonia Group.

The BCG funded the terrapins' expatriation to the Tuscan sanctuary, which was billed as a home for life, where the creatures could swim in lakes fed by streams warmed by volcanic rock. The sanctuary was also claimed to be "hermetically sealed" so that no red-eared terrapins could escape and start terrorising the native species.

Almost immediately, the BCG received evidence that terrapins were dying because the sanctuary's ponds were too small and because fencing was not secure. But the charity said it dispatched people to check on the animals' conditions and found no problems, so it continued to part-fund the project.

"It all sounded too good to be true, and it was," said Paul Eversfield, a former BCG member, referring to his visit to the sanctuary in the autumn of 2007.

Eversfield said that he found a muddy pond overcrowded with terrapins with no filtration, and fencing through which the creatures could easily escape. He said he warned the BCG of the situation.

Don Freeman, the BCG's chairman, said Eversfield's findings were not ignored. "When we sent people out to have a look, including those who had sent terrapins there, they were satisfied with what they found." According to Freeman it was difficult to prove that terrapins had escaped because feral red-eared terrapins were already at large in Tuscany before the sanctuary was built.

"The problems were none of ours. It was a question of [Ballasina's] tenure and that's it," added Freeman. "What can we do about another organisation? Nothing. It's up to them. The book is closed."

A former Carapax employee said the sanctuary "lost control" of its animals and "turtles spilled into streams, ponds and rivers, creating environmental pollution".

After a court battle with the local landowner, Ballasina was last year evicted from the site for breaking his tenancy terms. Native tortoises and turtles were seized by the Italian authorities but the non-native terrapins were left on the site and the Italian courts allowed Ballasina access to feed the animals. Ballasina could not be reached to put the allegations to him.

In a letter purporting to be from the Belgian based charity the International RANA Foundation, the umbrella group of Ballasina's defunct Carapax project, a representative accused "local mafia" of forcing the Tuscan centre to close, claimed reports of salmonella infections at the site were invented, and appealed for more money to pay to feed "8,000 turtles" still there.

Freeman confirmed the BCG was still funding the feeding of the terrapins left in the sanctuary from charitable donations, but insisted that the money – €180 (£157) a week according to the BCG's website – was no longer going to Ballasina or Carapax.

The Italian authorities appointed Marco Zuffi, of the Museum of National History, at the University of Pisa, to monitor the derelict sanctuary. According to Zuffi the sanctuary became overcrowded because Ballasina was incapable of refusing requests to help terrapins. "He should not have accepted so many individuals coming from the UK or other countries," said Zuffi. "He wasn't able to say 'no'." Observers who regularly visited the site said that the remaining 1,500 terrapins were in a "pretty bad" way, he said.

"The animals are evidentially very distressed. They come to the shore with their mouths open looking for food. It is a sign of animals in a very bad condition."

Eversfield said the remaining terrapins were a dilemma for all parties involved. "This solution to this is very uncomfortable. The site needs to be sanitised and we need to collect the animals and humanely destroy them," he suggested.

According to Zuffi, euthanasia was not a solution. "If you [tell] the public you are going to kill hundreds and hundreds of sliders you're likely to be stopped at all legal levels. People want to protect their pets, and sliders are considered pets."

He said that the terrapins could be repatriated to their countries of origin, including the UK (some are micro-chipped), or taken to secure centres. But he said that there was no timetable for cleaning up the sanctuary.